SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L001_R2_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 649.11 s (44 us/read; 1.36 M reads/minute). === Summary === Total reads processed: 14,686,084 Reads with adapters: 11,052,394 (75.3%) Reads written (passing filters): 14,686,084 (100.0%) Total basepairs processed: 2,202,912,600 bp Quality-trimmed: 8,170,892 bp (0.4%) Total written (filtered): 1,785,498,326 bp (81.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11052394 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 11.2% G: 23.2% T: 36.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2172306 3671521.0 0 2172306 2 315945 917880.2 0 315945 3 169586 229470.1 0 169586 4 102198 57367.5 0 102198 5 92121 14341.9 0 92121 6 78915 3585.5 0 78915 7 65916 896.4 0 65916 8 91966 224.1 0 91966 9 73557 56.0 0 73312 245 10 79999 14.0 1 76173 3826 11 83777 3.5 1 78744 5033 12 84445 0.9 1 79272 5173 13 92865 0.2 1 87504 5361 14 88444 0.2 1 82453 5991 15 72972 0.2 1 68400 4572 16 103628 0.2 1 97383 6245 17 83622 0.2 1 78153 5469 18 78826 0.2 1 74157 4669 19 100647 0.2 1 94372 6275 20 93537 0.2 1 88067 5470 21 82005 0.2 1 77188 4817 22 92897 0.2 1 87543 5354 23 95873 0.2 1 90242 5631 24 96154 0.2 1 90197 5957 25 107344 0.2 1 101210 6134 26 88692 0.2 1 83193 5499 27 96620 0.2 1 90107 6513 28 92786 0.2 1 88163 4623 29 97544 0.2 1 91712 5832 30 97471 0.2 1 92326 5145 31 103994 0.2 1 98068 5926 32 93992 0.2 1 89009 4983 33 103947 0.2 1 97692 6255 34 130356 0.2 1 123003 7353 35 75888 0.2 1 71960 3928 36 101074 0.2 1 95184 5890 37 109064 0.2 1 102746 6318 38 100719 0.2 1 95809 4910 39 99097 0.2 1 94226 4871 40 108626 0.2 1 102518 6108 41 105593 0.2 1 100195 5398 42 108346 0.2 1 102605 5741 43 99135 0.2 1 93859 5276 44 112964 0.2 1 106912 6052 45 120273 0.2 1 114139 6134 46 86822 0.2 1 82356 4466 47 107964 0.2 1 102668 5296 48 105861 0.2 1 100664 5197 49 110040 0.2 1 104589 5451 50 103888 0.2 1 98336 5552 51 130541 0.2 1 123943 6598 52 92963 0.2 1 88623 4340 53 111922 0.2 1 106898 5024 54 84092 0.2 1 80032 4060 55 108967 0.2 1 104198 4769 56 110137 0.2 1 104842 5295 57 104380 0.2 1 99728 4652 58 100352 0.2 1 95962 4390 59 101272 0.2 1 96515 4757 60 103619 0.2 1 98712 4907 61 107020 0.2 1 101830 5190 62 116477 0.2 1 111010 5467 63 153560 0.2 1 147083 6477 64 118136 0.2 1 113593 4543 65 80776 0.2 1 77236 3540 66 87168 0.2 1 83301 3867 67 85836 0.2 1 81942 3894 68 86253 0.2 1 82443 3810 69 84506 0.2 1 80622 3884 70 92306 0.2 1 88038 4268 71 90825 0.2 1 86927 3898 72 86185 0.2 1 82424 3761 73 89325 0.2 1 85551 3774 74 82222 0.2 1 78765 3457 75 77552 0.2 1 74138 3414 76 75204 0.2 1 71865 3339 77 74674 0.2 1 71463 3211 78 71366 0.2 1 68191 3175 79 67543 0.2 1 64632 2911 80 67004 0.2 1 64137 2867 81 66579 0.2 1 63792 2787 82 63260 0.2 1 60623 2637 83 59885 0.2 1 57259 2626 84 57771 0.2 1 55217 2554 85 56672 0.2 1 54103 2569 86 55528 0.2 1 53139 2389 87 54690 0.2 1 52283 2407 88 52598 0.2 1 50360 2238 89 46378 0.2 1 44318 2060 90 44805 0.2 1 42852 1953 91 41839 0.2 1 39962 1877 92 38539 0.2 1 36849 1690 93 36522 0.2 1 35046 1476 94 35648 0.2 1 34150 1498 95 33020 0.2 1 31626 1394 96 31039 0.2 1 29760 1279 97 28162 0.2 1 26958 1204 98 25327 0.2 1 24248 1079 99 23909 0.2 1 22911 998 100 21397 0.2 1 20519 878 101 19468 0.2 1 18700 768 102 18321 0.2 1 17542 779 103 16795 0.2 1 16092 703 104 15607 0.2 1 14948 659 105 13615 0.2 1 13013 602 106 12134 0.2 1 11629 505 107 10718 0.2 1 10267 451 108 9677 0.2 1 9284 393 109 8561 0.2 1 8182 379 110 7592 0.2 1 7242 350 111 6810 0.2 1 6531 279 112 6017 0.2 1 5741 276 113 5139 0.2 1 4918 221 114 4338 0.2 1 4134 204 115 3645 0.2 1 3478 167 116 2960 0.2 1 2807 153 117 2433 0.2 1 2312 121 118 2180 0.2 1 2058 122 119 1702 0.2 1 1624 78 120 1461 0.2 1 1377 84 121 1230 0.2 1 1157 73 122 1031 0.2 1 968 63 123 857 0.2 1 808 49 124 756 0.2 1 706 50 125 617 0.2 1 580 37 126 477 0.2 1 448 29 127 390 0.2 1 359 31 128 303 0.2 1 291 12 129 226 0.2 1 207 19 130 179 0.2 1 161 18 131 150 0.2 1 142 8 132 131 0.2 1 123 8 133 129 0.2 1 118 11 134 199 0.2 1 187 12 135 112 0.2 1 107 5 136 50 0.2 1 48 2 137 54 0.2 1 49 5 138 38 0.2 1 37 1 139 28 0.2 1 24 4 140 20 0.2 1 18 2 141 13 0.2 1 12 1 142 11 0.2 1 10 1 143 8 0.2 1 7 1 144 5 0.2 1 3 2 145 4 0.2 1 3 1 146 7 0.2 1 3 4 147 20 0.2 1 18 2 148 18 0.2 1 17 1 149 13 0.2 1 11 2 150 93 0.2 1 85 8 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L001_R2_001.fastq.gz ============================================= 14686084 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 11190 (0.1%)